Posted
by
Unknown Lamer
on Friday May 27, 2011 @04:45PM
from the sewer-shark-comes-true dept.

Antipater writes "Slashdot readers may remember the announcement and ensuing controversy six months ago over the NASA discovery of microbes that can supposedly incorporate arsenic into their DNA. Now, The Washington Post reports that Science has published a collection of eight scathing critiques of astrobiologist Felisa Wolfe-Simon, her methods, and her conclusions. Wolfe-Simon is starting to fire back and gather her own allies — one wonders if we're in for another cold-fusion style science war."

Running the same code to get the same model results is not "duplicating scientific results". It's running the same program and getting the same output. Ditto for plotting the estimated average temperatures for the last 200 years. Running gnuplot or matlab on someone else's data and getting the same plot isn't science.

Duplicating a scientific result would mean that you take the same starting conditions, do the same process, gather your own data, and get the same result -- with different objects. And it incl

I'm so tired of people saying this -- if you can't replicate an experiment with the same starting conditions then it's not science -- that it total and complete bullshit.

Science works like this:
Step 1. Formulate a hypothesis.
Step 2. Test the hypothesis.
Step 3.
If hypothesis checks out, repeat step 2. After sufficient iterations call it a theory.
If hypothesis doesn't check out, throw it out and formulate a new hypothesis.

*no where* in the above does it require you to have the same starting conditions. In the case of global warming the hypotheses are of the form "Higher levels of CO2 in the atmosphere will lead to higher temperatures". There are *many* ways you can test these hypotheses -- you don't need to have a model earth to play with.

*no where* in the above does it require you to have the same starting conditions.

Not defending GP's erroneous claim (while I think there are legitimate criticisms of AGW as it's being fed to us, not having a "Control Earth" isn't one of them), but the point could be argued that, in many cases, step 2 would imply "under similar conditions" (since "exact same conditions" is nearly impossible even in a controlled experimental environment.)

Well, the fact that we never get identical conditions is covered by the theory of errors. Don't see how similar conditions are not present in climate science. The basic point is, after all, to make a prediction and see if it comes true. That's what is happening.

Well, the fact that we never get identical conditions is covered by the theory of errors. Don't see how similar conditions are not present in climate science. The basic point is, after all, to make a prediction and see if it comes true. That's what is happening.

While the basic point may be "to make a prediction and see if it comes true", part of that prediction has to be the null hypothesis if you are going to do real science. That's the part that is NOT happening.

It's really easy to predict that "if Mindcontrolled is alive on this planet the temperatures will go up" and gosh, look it came true! Using current global climate change science, I've just proven that YOU are the cause of global warming, and all we need to do is get rid of you to solve the problem.

You are aware that there is not only a statistical connection between CO2 concentration and temperature, but also a physical mechanism that you can test in the laboratory? In your analogy - the tribesman actually took a look at the wiring of the car and found that the radio is not wired into the starter circuit? I can measure the IR spectrum of CO2, actually, I, personally DID measure it. Physical chemistry lab II, back then, before the war. We also know the mechanism of radiation equilibria. As to the Mind

You are aware that there is not only a statistical connection between CO2 concentration and temperature, but also a physical mechanism that you can test in the laboratory?

I'll take it from this question that you disagree with my proven hypothesis that you are the cause?

Yes, I am well aware that in the laboratory you can prove quite a lot of things. What you cannot do in the laboratory is test all of the competing and counteracting systems involved in something as large as the earth. A three foot sealed box in the lab does not map well into an experimental domain as large as the planet.

In your analogy - the tribesman actually took a look at the wiring of the car and found that the radio is not wired into the starter circuit?

He didn't have to. It was trivial to fully test the hypothesis that the radio had to be

Even the most rabid AGW modeler supplicated at the alter of Gaia the CO2 is a minor player that only causes minor warming a some humidity increase and it's the amplification the cause by the increased water vapor that does the heavy lifting in AGW models.

There is a point where you should realize that the hole you dug yourself into is deep enough by now. Strawmen over strawmen. Where do I say we know everything? That's right. Nowhere. And if you seriously deny CO2 trapping IR as the main mechanism of the greenhouse effect, then please explain to me why the radiation equilibrium between incoming sunlight and outgoing blackbody radiation puts the global average temperature at about 20K less than observed when you do not take CO2 into account. As for your "hypo

I've run IR spectrometers a few times, myself. Very nice rotational and vibrational lines from CO2. But that does not prove a hypothesis that "increased CO2 concentration in the upper atmosphere will cause increased temperatures". That's only one tiny part of an immense system.

Of course it does! What else would you conclude from it? An increase of gravity causes a stone to accelerate faster (to fall faster). For that you don't need experiments. If you had physics in school, you KNOW that.

The problem is that the defenders of AGW are saying we should cut back on CO2 emissions through a complex scheme of geo-political government control of people's activities. In effect, creating a world government:

Quote by Ottmar Edenhoffer, high level UN-IPCC official: "We redistribute de facto the world's wealth by climate policy...Basically it's a big mistake to discuss climate policy separately from the major themes of globalization...One has to free oneself from the illusion that international climate po

But what do you mean "under similar conditions"? Over interpreting "under similar conditions" is equivalent to throwing away induction.

And if you're willing to throw away induction then we need to say goodbye to all of science. Past experiments show that apple's fall to the ground, but none of these experiments have been conducted in the year 2012. Therefore saying that apples will continue to fall to the ground in 2012 is an unscientific statement.

By "Under Similar Conditions" I mean, for example, two sealed test chambers, one for the "control" and one for the "experimental." Even if designed, engineered, and built to identical specifications, the "universal human imperfection law[0]" says that there is going to be *some* difference between the two chambers, no matter how small.

Get out of your armchair and actually look at examples of the models predicting unknown phenomena, I'll give you a head start, polar amplification, stratospheric warming.

current GW studies are mostly not science, but political PACs.

Give me one example of a political PAC actually creating a model, I would be especially interested in seeing an anti-AGW PAC's computer model since AFAIK no such beast exists. Hint: The IPCC is not a PAC nor does it do any reasearch beyond assesing the published litrature.

Yet they are being claimed valid and final - hence current GW studies are mostly not science, but political PACs.

It is the oposite around. The anti global warming propagande spread by the Bushs legislatives is not science. Every sane scientist knows since 45 years or longer about GW. Just the USA government ignored it constantly and even started to argue against it and funded pseudo science Anti-GW movements and publications.

I'm so tired of people saying this -- if you can't replicate an experiment with the same starting conditions then it's not science -- that it total and complete bullshit.Science works like this:Step 1. Formulate a hypothesis.Step 2. Test the hypothesis.Step 3.If hypothesis checks out, repeat step 2. After sufficient iterations call it a theory.If hypothesis doesn't check out, throw it out and formulate a new hypothesis.

Isn't the repeat step 2, replicating the experiment? The real technique in the climate models testing is actually called backcasting, they set the models to the initial conditions of lets say 1980 run through 30 years of model run then the results should be about what we have today, that's why paleoclimatetology is so hotly debated, and especially why how the thermometer records are adjusted is almost enough to start a shooting war.

Science works like this:
Step 1. Formulate a hypothesis.
Step 2. Test the hypothesis.
Step 3.
If hypothesis checks out, repeat step 2. After sufficient iterations call it a theory.
If hypothesis doesn't check out, throw it out and formulate a new hypothesis.

Isn't it more accurate to say

Science works like this:
Step 1. Develop a theory based on what you know so far.
Step 2. Formulate a hypothesis that would be true of the theory is valid and/or would be false if the theory is not valid (or vice-versa).
Step 3. Test the hypothesis.
Step 4a. If hypothesis checks out, repeat step 2.
After sufficient successful iterations call it an established theory.
Step 4b. If hypothesis doesn't check out, modify the theory and go back to step 2.
If that doesn't pan out after sufficient attempts, throw out the theory.

Yes, that is more accurate. And an even longer, more accurate description could be come up with as well.

But scientists don't sit around figuring out ways to apply the scientific method -- it's a general guideline, not a flowchart, but their work (at least good science, that is) tends to fall into the same general flow.

Bad science, that's another matter entirely. There, people seem to start with a proposal -- "I want to show that X is true" and then cherry pick their data to do so. Unfortunately, this see

Nice way of showing that you didn't remotely follow the science there. Protip: Watts is not part of it. There are multiple data sets, multiple models, a strong, controversial discussion about the building of said models - and still, a consensus on the basic facts, because they are bloody obvious by now. If you think reproducibility means "taking two different earths", you don't have the slightest grasp about what science actually is. This is actually so exceedingly dumb that i fail to grasp how someone can come up with that argument.

I don't know how many times I have to say this; perhaps people like you will one day get the message: running a model is not the same as performing an experiment. If all models have the same bias, then you cannot claim they are correct just because they come to a consensus.

You don't have a clue. You don't need a different planet to figure out that increasing CO2 concentrations in an air sample increases its absorption of IR wavelengths. Plenty of tests that can verify that.

Your standard of what constitutes science is so ridiculously far out there that it would be impossible to figure anything out about anything that is bigger than a science lab. Thankfully, most scientists have figured out that lab experiments provide a nice basis with which to predict larger phenomena.

And if you really think that that's the only way that discoveries can be made about planet-wide phenomena, please ignore weather reports, tsunami warnings, volcano warnings, earthquake reports, oil discovered through seismic evidence.... yeah, scientists who don't have a second earth to work with have really not contributed anything to society.

You don't have a clue. You don't need a different planet to figure out that increasing CO2 concentrations in an air sample increases its absorption of IR wavelengths. Plenty of tests that can verify that.

Data point: Arrhenius figured out the physics of greenhouse gasses a hundred years ago.

But GWDs don't want to discuss mechanisms that are long established facts; they want to identify some model that they think they can cast doubts on.

Very like creationist rhetoric, actually: Avoid the core issues, offer arguments where you think you can cause a few to doubt.

You don't have a clue. You don't need a different planet to figure out that increasing CO2 concentrations in an air sample increases its absorption of IR wavelengths. Plenty of tests that can verify that.

If all the entire earth/atmosphere/ocean/sun system is to you is "an air sample with some CO2 in it", then you've missed the point entirely and there is nothing I can say that will make any difference to you.

People who oversimplify a complicated system so they can understand a small part of it often get it wrong on the larger scale.

yeah, scientists who don't have a second earth to work with have really not contributed anything to society.

The people who blather such ridiculously twisted interpretations of what someone else has said are the ones who fail to contribute. You'll find nothing like what you said in a

Running the same code to get the same model results is not "duplicating scientific results".

I guess your code tells you that the world's glaciers aren't really melting.

Maybe you weren't aware that we've got more evidence for global warming than someone's plot of historical temperatures.

For global warming, it means taking two different planet Earths, adding CO2 to one and not the other, and then measuring the temperatures.

You sound like a creationist: regular science is OK (and works), right up until it concludes something you don't like, and then you start demanding the impossible so you can convince yourself that regular science isn't really science, and your beliefs trump the evidence.

You sound like a creationist: regular science is OK (and works), right up until it concludes something you don't like,

I'll point this out just once and then let you ramble on. I neither like nor dislike the conclusions coming out of "global climate science", I merely accept them as hypotheses that are not truly tested to the degree science demands. I have no problem with a scientist who says "I think" or "we believe". What I dislike are the "scientists" who claim "it is proven, there is no further debate necessary."

Now please proceed with your rants about things I didn't say. Knock yourself out. Keep throwing in a person

Scientists have never, in a laboratory, observed a strain of single cellular organisms gradually mutating into a complex multi-cellular animal.
Does that mean you consider Evolution to be "not truly tested to the degree science demands" too?

Smart decision. Smarter yet would have been to just point it out zero times.

If you were half as interested in learning how science really works as you are in having an excuse for rejecting aspects of reality that you don't like, you could make a long, long, long list of things that scientists study rigorously, despite not being able to reproduce them in the laboratory.

For global warming, it means taking two different planet Earths, adding CO2 to one and not the other, and then measuring the temperatures. Can you show me the referreed journal article that describes that experiment being done even once, much less in a reproducable manner as required by the scientific method?

So according to your logic, Newton was just bullshitting when he said the Moon causes the tides because he did not have a control version of the Earth, not only that but every scientist since the 1600's has unquestioningly swallowed Newton's unscientific theory about tides.

But even if your "logic" made sense, it is moot since there are many independent data sets [realclimate.org], and there is a physical explaination that you can test yourself with some cheap lab equipment. If the physical explaination is wrong then it means spectroscopy is wrong, which in turn means much of quantum mechanics is wrong, astronomy is wrong, ect. And if you really want to look at other planets (as climate scientists such as Hannsen already have), then please explain to us why the surface of Venus, (AKA our sister planet), is hot enough to melt lead.

The other major faw in your post, is that you don't seem to realise the physics came first (Fourier 1824), then the prediction of AGW based on the physics came in the 1890's, then strong evidence of increased CO2 forcing was found in the temprature records in the late 50's. Then computer models started making many other predictions about the effect of increased CO2 such as polar amplification and stratospheric cooling that have since been confirmed by observations.

I put it to you that you are acting no differently to a creationist when you choose to denigrate an entire branch of science based on ill informed assumptions and your own personal definition of the scientific method, or perhaps your just further evidence of the Dunning-Kruger effect [wikipedia.org].

Yes, and as you know the doubling of CO2 should produce approximately 1C of warming. All of the rest, including your stupid link to "realclimate" (a marketing site for discredited activist scientists like Michael Mann), is conjecture based on no evidence whatsoever.

For global warming, it means taking two different planet Earths, adding CO2 to one and not the other, and then measuring the temperatures. Can you show me the referreed journal article that describes that experiment being done even once, much less in a reproducable manner as required by the scientific method?

I dissagree:first of all, we know that CO2 is a greenhouse gas. So it should be completely logical that an increase of CO2 concentration leads to an increase of the overall temperature. Nevertheless you

Err, no. What you are describing is some kind of rationalist/skeptic myth of science, not science as it has been done for the past three hundred years. Not the science that has explained the motion of the wandering stars and the tides, built flying machines and novel power plants, taken us to the Moon and back.

Universal gravitation does not meet your criteria. "Sorry, Mr Newton. You have to take two masses, one with inertia, one without, and compare their gravitational attraction. Otherwise you aren't

One of the basic principles of the scientific method is the ability for peers to independently reproduce results. If this is not the case, then this is not science.

if that's the case then global warming is not a science.

Global warming is a science and can, in fact, be tested and proven independently. The issue is that most of us would rather we not prove it a first time here on Earth, let alone create another Earth and test it twice.

(There are some experiments that can't be carried out because we don't have the tools ; there are some that can't be done because we don't have the environments (like this one) ; and there are some that we don't have the materials for (e.g. determining which would have won in a Tyrannosaurus vs Giganotosaurus contest). At which point, you have to use modelling. Unless you've got a spare planet in your

Quote by Ottmar Edenhoffer, high level UN-IPCC official: "We redistribute de facto the world's wealth by climate policy...Basically it's a big mistake to discuss climate policy separately from the major themes of globalization...One has to free oneself from the illusion that international climate policy is environmental policy. This has almost nothing to do with environmental policy anymore."

Quote by Club of Rome: "In searching for a new enemy to unite us, we came up with the idea that pollution, the threat

It's easier to shoot the messenger then the message. But it's even easier to shoot the message then carry it on if you don't like change. Peer review has seemed to of went form, "Yes, we did it too", or "no, it didn't work for us", or even a "we saw something a bit different when we tried it", to an "I agree or disagree, let's take a vote on it". At least in some things anyways.

While you are right, that's how science works and if it isn't working that way, it isn't science, but this non-science is happening

"Further, Wolfe-Simon has provided samples of the supposedly arsenic-loving microbes to “four or five” independent scientists, she said, who are now trying to prove her wrong — or maybe just show that she was right."

This looks to me the scientist is giving out samples of the said bacteria to other scientists to try reproducing the findings.

In this case, it looks like Wolf-Simon published her results, and some peers fired off some immediate critiques of her methods, while others raised questions based off of what is already known of molecular biology. Wolf-Simon is responding to 8 of these criticisms in the latest publication of Science. As far as I can tell, no one has attempted (and succeeded or failed) to reproduce Wolf-Simon's results. There hasn't been a whole lot of time to do the necessary studies.

As far as I can tell, this is science, as she is performed. You publish controversial/novel results, people immediately try to pick your results apart, and you respond to them. In an ideal world, everything would be done with the same level of rigor as these results are being handled, not just the "hard sciences".

Pretty much how it works. At this point, you do methodological criticism. Everyone gets hit with that - in most cases it doesn't get that public, though. That's the price you pay for doing press releases in that scope. I personally just got my publications ripped apart in pretty much closed conferences. Reproducing it comes later - establishing a system to work with weird extremophiles takes time. The tests for reproducibility will take a couple of months more and burn up some PhD candidates, as usual... Th

At this point, I would not conclude that anything is wrong with the original research - only that more experiments are needed. Pretty standard. No peer reviewer tries to reproduce experiments, usually. They just offer methodological criticism. And the criticism offered so far could pretty much be overcome by some discussion with the reviewer. The original research is not the strongest, but neither is the criticism. It is interesting enough stuff to publish it, if only to get the discussion going and more people interested in picking up the subject. I see no failure there. Business as usual.

One of the basic principles of the scientific method is the ability for peers to independently reproduce results. If this is not the case, then this is not science.

You presume that the critics have attempted to independently reproduce the results. They have not. They are merely identifying potential sources of false positives. While the original team would be wise to explain how these potential sources of error were already addressed, and if necessary to run additional experiments addressing lapses or unconsidered factors, hypothetical arguments as to why an experiment cannot have worked do not prove that the results cannot be reproduced and/or are actually caused by other mechanisms.

"The exchange does not put forth new data on the matter, but centers on the original experiments in which Wolfe-Simon isolated bacteria from arsenic-laden Mono Lake, California, and then tried to grow them in cultures with large amounts of arsenic and no phosphorus, which is typically required for growth."

Nobody has tried to reproduce the result.

"University of British Columbia microbiologist Rosie Redfield, the blogger most critical of Wolfe-Simon both personally and professionally, asserts in one of the Technical Comments that Wolfe-Simon did not go far enough in purifying DNA from GFAJ-1 before testing it for its arsenic components."

Valid criticism, but not proof of irreproducability or alternate mechanism.

Extraordinary claims require extraordinary proof. On the other hand, scientists claiming that things are impossible have routinely been proven wrong. Unless something is shown to violate well established laws, hypothetical criticism is usually far less valuable than actual experimentation and reproducible alternate explanation.

You can be sure that they are trying to reproduce it - it just takes time. Establishing a completely new system takes not weeks but months or years and leaves some PhD candidates along the road. We'll see more definitive data next year or so.

This conduct on the part of the science community is pretty non-scientific, IMHO. If you have doubts, attempt to reproduce the original results. In doing so, you will either reproduce them and if not, you may stumble upon scientific proof of precisely why the original experiment is flawed. If the original research stands to overturn a century of accepted theory, then you had *better* bloody well attempt to verify or contradict the original research using the *scientific method* instead of using 100 years of possibly flawed theory as a shield against new knowledge and insight. Personal attacks? Are you kidding me? Are these people children?

Carl Sagan is turning in his grave.

Peer review does not normally involve attempting to replicate someone's results. It involves reading carefully to see whether they did their homework, whether the (purported) observations support the claims, whether they forgot to take something important into account, etc.

If you do publish something that is new or surprising, other researchers will jump all over it. But everyone has more to do than they can finish in one lifetime, so no one is going to run out and try to replicate results until some case has been made that they are plausible.

You could waste lifetimes trying to reproduce results you have doubts about.

First someone publishes.Then their peers (other scientists) read the study and critique it. Some criticism will be sent direct to the authors, others will be published.The author reads the criticisms and responds, hoping to address the critics' concerns and shore up support for their article.IF they can't address the criticisms, the study is abandoned.IF they do manage to keep their study in good repute, it becomes a valid part of the scientific canon- and othe

It is not even a matter of reproducible results. This whole affair is a logic exercise, the experiments performed cannot rule out other trivial explanations for the results. Science does not only require an experiment showing the plausibility of one explanation, but also the implausibility of alternative reasonable explanations.

We're not, because the organisms are just a variant on the same theme as other life. It was an over-the-top unsustainable claim, a bunch of molecular biologists who actually are experts in the field caught it, and that's that.

The original article presented an exception to one of the fundamental rules of life on Earth. To survive, microbes, plants, and animals all require six essential elements: oxygen, carbon, nitrogen, hydrogen, sulfur, and phosphorus.

So please answer this questions:

How many of those elements are used by the life forms found at the hydrothermal vents at the bottom of the ocean?

What is the make up of their DNA?

Oh and I must say; life does not give a shit about man made rules and how we think it should b

Uh, you do realize those "man made rules" are based on observation. Extensive and thorough observation. Basically, the need for oxygen, carbon, nitrogen, hydrogen, sulfur, and phosphorus to sustain life has been demonstrated not just at the organismal level, but also at the molecular level, with predictable and repeating patterns in every life form ever studied. That is the definition of a "Law" in science. Something that is assumed to be a fact because exceptions have never been observed. It, of course, do

And octopus' as well as some other sea creatures have copper based blood as well.See: http://en.wikipedia.org/wiki/Hemocyanin [wikipedia.org] they list some animal families with coper based oxygen transfer.

They're claiming there are flaws in the methodology. If they're right and someone else follows the same flawed methodology, then that result is no more valid than the original result. You want the original authors and anyone attempting to replicate their results to eliminate the potential for any flaws, so somebody's got to raise the possibility. That's the stage they're at now: raising possibilities.

Extraordinary results require extraordinary evidence.
Disregard personal attacks on Wolfe-Simon, consider comments and considerations on the methods, etc of the work itself, and allow a few years for additional research to support or refute.
Most of all keep calm, it's not war, it's just science.

Your wit is scalding. Now how about learing some facts, so you can use it to some useful end? Starting point: The scientific community does not give a rats arse about Al Gore or the left. Don't burn yourself on those strawmen.

It's a normal part of the scientific process. Holding a PhD in Biochemistry myself, with focus on Biophysical Chemistry, and I kinda agree with your son there. Interesting data, but needs some more rigor. But, well, that is not unusual - works like this all the time. We'll see more papers on this soon, then we'll learn more.

They are just doing their job as scientists. Science is supposed to embrace new ideas slowly. Otherwise we'd be running around believing in N rays [wikipedia.org] and whatnot. Granted, this is a cruel environment to come up with new ideas in, but it's still very much a necessity.

Thank you; I was about to point this out. Mod Parent Up, as the saying goes.

This is how science works, and how it has always worked. You hang your theory out and the rest of the scientific community goes for it with machetes and chainsaws, which either kills it or makes it stronger. That's how we sift the truth from the wishful thinking (and, more rarely, deliberate fraud). That's also why the idea of a "vast conspiracy of scientists" occasionally mooted by (cough) certain persons is so hilarious. It's about as feasible as throwing a dozen pissed-off cats into a large sack and finding that they all decided to enter into a conspiracy.

And thanks for reminding me about the N-rays; I read the famous Nature paper the other week, and (being a scientist) had great fun watching the poor bastards' theories being shredded in deceptively bland scientific prose.

That's how it should work, but sometimes there is a premature hardening of consensus and the whole scientific community may believing nonsense for decades on end. Commonly believed theories need to be tested and challenged, too - but funding and social/ peer review concerns often make thatt difficult, particularly in the softer sciences.

But I would venture a guess that the scientists who are so vocal about her findings are the very same scientists that rationalize silly things like God and Creationism in their own minds. After all, the existence and viability of arsenic-based life would be an affront to their own distorted views on the origins of life as we know it today.

I think that I would fair fairly well, as the microbe in question would have only a small amount of resources to colonize me. Arsenic based life requires a substantial amount of arsenic to exist--same with sulfur based life or anything else (though there is much more free sulfur available than arsenic in the earth's general environment). This reference may be helpful: http://en.wikipedia.org/wiki/Abundance_of_elements_on_Earth#Abundance_of_elements_in_the_Earth [wikipedia.org] (there's also a section on the human body on t

True. Small nitpick, though - they wouldn't compete against carbon, but against phosphorus. They are still carbon based, but supposedly work with As instead of P in their DNA and in their energy metabolism.